As the Trojan horse furore in Birmingham continues, and spreads, five issues emerge that require urgent national attention. First our system of school governance is broken and needs a total overhaul: its weaknesses contributed significantly to the real and imaginary problems in Birmingham. Second, the role and power of the education secretary needs to be reduced and his relationship with Ofsted clarified – neither can be trusted to act efficiently or fairly. Third, Ofsted itself needs to set out its working methods more openly if it is to retain the respect of those it inspects. Fourth, the place of religious bodies and their organised faiths in schools needs to be understood and reframed. Finally, there is an urgent need to provide help to the schools involved in the Trojan horse affair to avoid enormous damage to their pupils' education and community cohesion.

Consider. Governors can and do misbehave. When they exceed their brief, usually colleagues quickly remind them of the respective roles of governors and school professionals. Just occasionally, however, a bullying clique forms and causes mayhem, especially for headteachers and leadership teams. In my 10 years in Birmingham there were a handful of occasions when this happened. Invariably the motivation of the governors was commendable, namely to accelerate improvements in outcomes for their children. As senior officers, with the help of local councillors and the cabinet member concerned, we would spend many evenings in schools, community venues and Balti houses seeking better understanding of the way forward with both governors and community members on the one hand and headteachers on the other. On one occasion, we dismissed the governing body and set up an interim executive board, changed the school leadership and started again. We commissioned an independent report that helped us improve governor training and think carefully about the vital role of local authority governors. We established a whistleblowing protocol.

So great have been the recent cuts in local authority expenditure that Birmingham and many other local authorities have neither the resources nor sufficient senior and experienced staff to carry out their role effectively. Worse, the arrival of academies and free schools has created an open season for lay people and professionals keen to pursue their own eccentric ideas about schooling: and when trust or governor vacancies occur, some perpetuate the very English tradition of inviting friends to join them. When the community is white it doesn't cause much comment. In mono-ethnic east Birmingham, however, it is seen as a Muslim plot to expose pupils to an undefined "extremism".

In short, the weight we are putting on voluntary governors in autonomous schools is too great for them to bear. We are the only developed country to rely on a governing body system. If we want to avoid future scandals, some form of local democratic accountability for all schools, separate from governors, is urgently needed. The locally elected authority, if properly resourced, is the obvious existing vehicle for doing that.

That brings us to the excessive powers of the secretary of state. When I was born she had but three, one of which was the removal of air-raid shelters. Now he has more than 2000 including control through private contracts of free schools and academies, where he has the right to send two officials to any meeting of the governing body. This he failed to do in Birmingham with disastrous consequences. Indeed if any single person is to blame for the present turbulence, it is Michael Gove. It is extraordinary he did not exercise his right to send officials to Park View academy but leapt straight to asking Ofsted to inspect. Of the 21 schools inspected, five of the six found to be inadequate are academies controlled by Gove. Yet he has diverted the main blame on to Birmingham city council, in fact to anyone other than himself. Perhaps he worried – rather late in the day – whether the apparently Islamophobic undertones in his book, Celsius 7/7, should have persuaded him to step aside, as it would those of us with long experience in the public service, and leave the resolution of the issues to his deputy, David Laws.

More generally, so much centralised control is unhealthy in a democracy: the education secretary's power "has increased, is increasing and ought to be diminished" (to quote Baron Ashburton).

That brings us to Ofsted, which Gove summoned after he had failed both to act as he should and to call Birmingham to account for the stewardship of its own community schools. There is a host of questions for Ofsted. What did the commissioning letter from Gove ask? Who were the inspection team and what was their experience and knowledge of the issues? Were they accompanied by HMI national experts? What was their common guiding brief and how did it define signs of "extremism" and "radicalisation"? Did they stick to their tradition of reporting only on what they saw and ignoring hearsay evidence? How systematically did they collect the views of parents? What were communications between the Department for Education and Ofsted during the process? These should be easy questions to answer for Ofsted, which boasts a "commitment to transparency" as one of its guiding principles.

Trojan horse raises a fourth and even trickier question, namely the place of religion in schools. In Birmingham there are nine secondary and 51 primary aided Catholic schools, but just two Muslim aided schools. Equity demands there should be more, since there are as many Muslims as Catholics in the city and faith is important to each community. Some would argue against state aided faith schools. Recently I watched a presentation at a Catholic secondary school staff training day of its faith mission. As I mentally substituted "Muslim" for "Catholic" and "Allah" for "God" with each slide that appeared on the screen, I had little doubt about what a furore such an amended set of slides would cause in our Islamophobic society. Would inspectors ask whether the children in Catholic schools are being prepared suitably for life in modern Britain? But there is a long tradition of aided schools here and perhaps we should ask parents where there are over 90% Muslim pupils if they would like to become an overtly faith school.

What is urgently needed, however, is an end to the requirement to have a daily act of worship "wholly or mainly of a broadly Christian character" in community (non-faith) schools and academies. The right of heads to seek a "determination" to change that was often a source of friction between them and Muslim governors in a predominantly Muslim school. It led the community quite naturally to think that religion, apart from the agreed syllabus, had legitimate wider influence on the curriculum. It does not. Legislation is now needed to replace the act of worship clause with the need to promote pluralism and respect for those with different faiths and none, while making sure that schools stand for those values that underpin a peaceful and civilised society.

The final point is the most serious. Incalculable damage has been inflicted on the Birmingham schools caught up in this affair and to their pupils and parents. There are already acute staff shortages which will get worse. The way the affair has been handled is entirely down to Gove and Ofsted. They should provide extra resources and staff to mitigate the damage to the children and community in Birmingham. As they pick up the pieces they will probably never forget what's been done to them. One hopes they can bring themselves in time to forgive. They will be more likely to do so if they are given some help, in recompense for the injustices they are suffering. What the proud city of Birmingham needs least is to be treated as a colonial outpost of London; the solution to the problem lies in the former city, not the latter.

• Sir Tim Brighouse is a former chief education officer of Birmingham and schools commissioner for London